A feature that I think would be simple to implement and would hugely improve FlipaClip as an animation and drawing tool would be the Draw Behind option. This is something that is available in a lot of drawing and animation apps.
Essentially, each brush would have the option to be set to either draw normal or draw behind. When set to draw behind, any strokes made on the canvas would draw behind any existing strokes - as if you were drawing on the layer below.
This would mean you could make your line drawings and colour them all on one layer, and also add more colours without affecting previously added colours. Adding too many layers often makes things too complicated and, obviously, slows down the device - so this would be a nice way to improve, simplify and speed up the app.
In the attached example, this drawing could easily be made all on one layer, with the pen set to draw behind when adding the colours. The blue stroke shows how draw behind would work.